Log webserver changes (by Marleen Claeys if not specified elsewise) ------------------------ 2020/05/15 : Add new PWM databases - for use in MotifLocator and MotifComparison OK 12 new databses added based on collections from JASPAR_2020 OK parsing script (perl) stored in /var/www/html/MotifSuite/INCLUSive_for_users/CPU_64/applications/ OK Details on selection and profile parsing described in /var/www/html/MotifSuite/Jaspar_2020_PWM_selection_procedure.txt 2020/04/21 : Unification motifsuite_v2 - no functional change OK INCLUSive-3.2.2, 4.1.2, 5.2.0 -> common files and libraries unified into one source code OK Linking/compiling of unified motifsuite_v2 in Netbeans OK Linking/compiling of motifsuite_v2 on different servers (cyano/bioinformatics) OK Details on working with motifsuite_v2 described in /var/www/html/MotifSuite/motifsuite_v2_compile.txt 2015/04/20 : Transfer MotifSuite from PSB to INTEC PSB ~/webtools is transferred to /var/www/html/MotifSuite/ PSB ~/bioapp is transferred to /var/www/html/MotifSuite/readwrite/ Adjustments to individual files: Index.html: revisions date and version number webdesign.php : update figure/text to latest status config.php : adjusted to new location settings createbackgroundmodel.php : publications link to Gert's articles not active 21/04: HOLD: Issues with permissions to run the applications. 2014/03/13 : Update web interface link to the latest version (northomotifsampler.php) 2014/03/10: Install merged NOrthoMotifSampler+PhyloMotifSampler (release to 4.1.2) But keep link in noms-webinterface to NOrthoMotifSampler_yan for now. - Install NOMS and PHMS executable 4.1.2 release on : (32-bit not done for noa - only when releasing the standalones on webserver) (executables::64bit) (compile on /home/... on 'ssh vampire', then exit vampire and cp to www/group/...) OK /home/macla/m_MotifSuite/CPU_64/applications OK /www/group/biocomp/extra/bioinformatics_prod/webtools/MotifSuite/INCLUSive_for_users/CPU_64/applications (tar.gz::) OK /home/macla/m_MotifSuite/INCLUSive_backup OK /www/group/biocomp/extra/bioinformatics_prod/webtools/MotifSuite/INCLUSive_for_users/CPU_64/backup - MotifSuite: update Index.htm to refer to northomotifsampler_yan.php, upate further links to use northo_submitversioncheck_yan.php, northo_submitApplicationResult_yan.php 2014/01/22 : Upgrade NOrthoMotifSampler test release to 4.1.1 Install TEST release on : (executables::64bit) (compile on /home/... on 'ssh vampire', then exit vampire and cp to www/group/...) OK /home/macla/m_MotifSuite/CPU_64/applications OK /www/group/biocomp/extra/bioinformatics_prod/webtools/MotifSuite/INCLUSive_for_users/CPU_64/applications (tar.gz::) OK /home/macla/m_MotifSuite/INCLUSive_backup 2014/01/16 : release INCLUSive-3.2.2 : - debug in MotifRanking (fully reset MaskVector at every next PWM assessment) - revamp in MotifSampler (lean implementation of PSP - test phaze) Install new release on : (executables::64bit) (compile on /home/... on 'ssh vampire', then exit vampire and cp to www/group/...) OK /home/macla/m_MotifSuite/CPU_64/applications OK /www/group/biocomp/extra/bioinformatics_prod/webtools/MotifSuite/INCLUSive_for_users/CPU_64/applications (tar.gz::) OK /www/group/biocomp/extra/bioinformatics_prod/webtools/MotifSuite/INCLUSive_for_users/CPU_64/backup OK /home/macla/m_MotifSuite/INCLUSive_backup - not on sista anymore (executables::32-bit) OK /www/group/biocomp/extra/bioinformatics_prod/webtools/MotifSuite/INCLUSive_for_users/CPU_32/applications (legend::INCLUSive_read_first_rev15.doc) : OK /www/group/biocomp/extra/bioinformatics_prod/webtools/MotifSuite/INCLUSive_for_users/AttentionReadFirst OK /home/macla/m_MotifSuite/INCLUSive_backup 2013/11/17 : TEST phaze : add NOrthoMotifSampler-4.1.0 application to MotifSuite. OK Request to set 'apache' as owner for the upload-dir (/northomotifsampler_uploads and ../results). Install TEST release on : (executables::64bit) (compile on /home/... on 'ssh vampire', then exit vampire and cp to www/group/...) OK /home/macla/m_MotifSuite/CPU_64/applications OK /www/group/biocomp/extra/bioinformatics_prod/webtools/MotifSuite/INCLUSive_for_users/CPU_64/applications (tar.gz::) OK /home/macla/m_MotifSuite/INCLUSive_backup 2013/10/31 : update FC_compile.txt on how to compile FC on the UG server 2013/10/29 : installed debugged FuzzyClustering software (still version 5.2.0) Debug : fix throw error in InstanceSet::CheckDatadimension--RemoveLowProbIndividuals() (executables::64bit) OK /www/group/biocomp/extra/bioinformatics_prod/webtools/MotifSuite/INCLUSive_for_users/CPU_64/applications OK /home/macla/m_MotifSuite/CPU_64/applications (tar.gz::) OK /www/group/biocomp/extra/bioinformatics_prod/webtools/MotifSuite/INCLUSive_for_users/CPU_64/backup OK /home/macla/m_MotifSuite/INCLUSive_backup OK /users/sista/mclaeys/INCLUSive_for_users/CPU_64/backup (executables::32-bit) OK /www/group/biocomp/extra/bioinformatics_prod/webtools/MotifSuite/INCLUSive_for_users/CPU_32/applications (legend::INCLUSive_read_first_rev13.doc) OK /www/group/biocomp/extra/bioinformatics_prod/webtools/MotifSuite/INCLUSive_for_users/AttentionReadFirst OK /home/macla/m_MotifSuite/INCLUSive_backup OK /users/sista/mclaeys/INCLUSive_for_users/AttentionReadFirst 2013/10/09 : changed contact email adress in config.php (from to to ) 2013/09/10 : lowmem jobs on UG server stay in queue, all jobs must now be "highmem" disabled the use of /www/bioapp/MotifSuite/qsubshort.sh (renamed it to qsubshort.sh_out_of_use) changed job submission to highmem for all applications in /www/group/biocomp/extra/bioinformatics_prod/webtools/MotifSuite/submitApplicationResult.php 2013/09/06 : (Stephane Rombouts) added Tomato backgroundmodel (order 1,2,3,4) to Database (/www/group/biocomp/extra/bioinformatics_prod/webtools/MotifSuite/bg-thijs/) and added link (Solanum lycopersicum) in dropdown list of MotifSampler 2013/09/10 : (Marleen Claeys) also added link in CreateBackgroundModel, MotifComparison, MotifRanking, MotifLocator. 2013/09/11 : (Marleen Claeys) centralized the dropdown list into Dropdown_bgm.php ('include' in MS,MR,MC,ML,CBgM) 2013/05/14 : reload INCLUSive-3.2.1 : debug in MotifSampler (error in SetMotifLength in case of motifW > seqL) Install new release on : (executables::64bit) OK/home/macla/m_MotifSuite/CPU_64/applications OK/www/group/biocomp/extra/bioinformatics_prod/webtools/MotifSuite/INCLUSive_for_users/CPU_64/applications (tar.gz::) OK/www/group/biocomp/extra/bioinformatics_prod/webtools/MotifSuite/INCLUSive_for_users/CPU_64/backup OK/home/macla/m_MotifSuite/INCLUSive_backup OK/users/sista/mclaeys/INCLUSive_for_users/CPU_64/backup (executables::32-bit) OK/www/group/biocomp/extra/bioinformatics_prod/webtools/MotifSuite/INCLUSive_for_users/CPU_32/applications (legend::INCLUSive_read_first_rev13.doc) : not revised 2013/02/04 : new release INCLUSive-3.2.1 : upgrade in MotifLocator (rescaling factor against higher-order background frequencies instead of SNF, else reported rescaled instance scores may be higher than one). Install new release on : (executables::64bit) OK/www/group/biocomp/extra/bioinformatics_prod/webtools/MotifSuite/INCLUSive_for_users/CPU_64/applications OK/home/macla/m_MotifSuite/CPU_64/applications (tar.gz::) OK/www/group/biocomp/extra/bioinformatics_prod/webtools/MotifSuite/INCLUSive_for_users/CPU_64/backup OK/home/macla/m_MotifSuite/INCLUSive_backup OK/users/sista/mclaeys/INCLUSive_for_users/CPU_64/backup (executables::32-bit) OK/www/group/biocomp/extra/bioinformatics_prod/webtools/MotifSuite/INCLUSive_for_users/CPU_32/applications (legend::INCLUSive_read_first_rev13.doc) OK/www/group/biocomp/extra/bioinformatics_prod/webtools/MotifSuite/INCLUSive_for_users/AttentionReadFirst OK/home/macla/m_MotifSuite/INCLUSive_backup OK/users/sista/mclaeys/INCLUSive_for_users/AttentionReadFirst 2013/02/04 : submitApplicationresult.php : assign all applications(except CBgM) to highmem (qsublong.sh). -----